Blanket statements like that from dealers are flat out ridiculous! Just adding those things doesn't automatically void your vehicle's warranty on the whole. It is illegal to do so under the Magnuson-Moss act. With that said however the following do apply...
1) Car Alarm - this does effect your warranty on the vehicle's wiring harness and a few things such as the ignition because the alarm is wired into them. The alarm installer will modify your wiring and because of that they can basically void your warranty on those areas because you modified it. If you have wiring issues or ignition system issues it can lead to warranty issues for you getting them covered. While they are required by law to prove that the modifications caused the problems most arbitrators and judges will side with the mfg because things were modified.
2) Intake - I assume you mean a CAI like K&N or Volant. They absolutely can NOT void your warranty because you install one. Again that is illegal. If you have problems such as moisture and/or dirt entering the combustion chamber or oil system, that can be traced to the CAI, then they actually can refuse warranty coverage. Dirty/damaged air flow sensors that need replacing, rich fuel conditions caused by the CAI which can foul plugs, etc... also won't be covered. Any areas you modify to install the CAI also become void under warranty. They can NOT however just void your engine or vehicle warranty because you put a CAI on. If you throw a piston rod, bend a valve, a lifter collapses, or some similar issue they can't void your engine warranty because you have a CAI on. If they tried they would lose in court in a heart beat.
3) - Muffler. This is absolutely the most ridiculous one I hear of. The ONLY warranty that is voided by adding an aftermarket muffler is on the exhaust system itself where you actually modify it. Like the alarm issue with modifying the wiring if you modify the exhaust you cancel out your coverage on anything you modify. So, by adding the aftermarket muffler you lose coverage on the muffler and any pipes you cut into. Your cats and such should be uneffected.
You can't just modify the snot out of your truck and still keep your coverage but by the same token dealers can't void everything because you add a muffler. Lord give me a break.